Two-time Olympic gold medallist Shiffrin had already won last week's Super-G, ahead of her two stronger events, the giant slalom and slalom.
Tough conditions as Shiffrin takes bronze
Two days of rain, unseasonably warm weather and high winds made conditions difficult, with the start moved down to the reserve position.
Rebensburg coped best, clocking the fastest time on the first run with 1:00.91, 0.19 seconds ahead of combined silver medallist Vlhova.
Four-time World champion Shiffrin was slow on the first half of the course but made up time on the bottom section to go fourth and keep her world title dream alive.
The women struggled on the second run with some blown off line by strong gusts of wind.
Olympic downhill champion Sofia Goggia crashed out on the second run but was able to ski down unhurt after seeing her hopes of a second medal at these World Championships dashed.
France's Tessa Worley, seeking a record third giant slalom world title, finished down in sixth.
Shiffrin skied well on that second run and was guaranteed a medal when Norway's double PyeongChang silver medallist Raghnild Mowinckel failed to beat her total time.
Then came Vlhova who produced a solid descent to knock Shiffrin off top spot.
Rebensburg skied the first three-quarters of the course superbly to reach the final time check four-tenths up on Vlhova.
But the German, who was an agonising fourth in the Super-G, somehow lost over half a second in the closing stages and had to settle for second.
It meant Vlhova was champion.
Shiffrin and Vlhova - A loving rivalry in the making
Vlhova has emerged as the main threat to the American's dominance of the technical disciplines, winning four World Cup events this season.
She also ended Shiffrin's run of seven consecutive World Cup slalom wins in Flachau, Austria last month.
But their growing rivalry has also been marked by some touching moments, including a caring embrace from the PyeongChang 2018 giant slalom winner in the build-up to these World Champs.
Why Shiffrin and new World Champ Vlhova are the best of rivals
Why Shiffrin and new World Champ Vlhova are the best of rivalsPetra Vlhova took World giant slalom gold in Are with Shiffrin third. And the pair's respect is clear from their recent interactions.
At 1.80m, Vlhova is tall for a female alpine skier and has thrived under coach Livio Magoni who guided Tina Maze to two Olympic gold medals.
She first came to global attention with slalom gold at the 2012 Winter Youth Olympic Games in Innsbruck.
REWIND: Petra Vlhova wins slalom gold at Innsbruck 2012 YOG
REWIND: Petra Vlhova wins slalom gold at Innsbruck 2012 YOGSlovakia's Petra Vlhova won gold in the women's slalom event at the Innsbruck 2012 Winter Youth Olympic Games. Re-live her second run here.
Rise to the top
Vlhova claimed her first World Cup win in the Are slalom in December 2015 and now has eight in total.
But, speaking to Olympic Channel this week in Are, Vlhova said she was most amazed at winning the Semmering giant slalom in December.
She said, "This for me was an amazing victory because [it was] first podium in giant slalom.
"My discipline, my strong discipline, is slalom." - Petra Vlhova talking to Olympic Channel
Having stopped Shiffrin in the giant slalom, can she deny the American a fourth consecutive world slalom crown?
She will certainly be confident of claiming her third medal of these World Championships in what should be a thrilling contest on Saturday.